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Input Variations: On this page, you must input variations file(s).
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Change chromosome notation for variations: On this page you can change the chromosome notation for variations.
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The following parameters are available:
Replace prefixes Input the list of chromosome prefixes that you would like to replace. For example "NC_000". Separate different prefixes by semicolons. Replace by Input the prefix that should be set instead, for example "chr". - SnpEff Parameters: On this page you can modify SnpEff parameters.
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The following parameters are available:
Genome Select the target genome. Genome data will be downloaded if it is not found. Cannonical transcripts Use only cannonical transcripts HGVS nomenclature Annotate using HGVS nomenclature Annotate Loss of function
Annotate Loss of function (LOF) and Nonsense mediated decay (NMD) Annotate TFBSs motifs Annotate transcription factor binding site motifs (only available for latest GRCh37) Upstream/downstream length Upstream and downstream interval size. Eliminate any upstream and downstream effect by using 0 length - Output: On this page, you need input output parameters.
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